Пример #1
0
def newPipeline():
    checkArgumentMarkerReducer()
    m = DnaUtils.readIUPACFile(sys.argv[1])
    mapOligos = DnaUtils.readOligosFile(sys.argv[2], m)
    # for k in mapOligos:
    #     for e in mapOligos[k]:
    #         print(e)
    # sys.exit(1)
    readSingleFastQFile(sys.argv[4], 10, "log.txt", mapOligos, sys.argv[3])
Пример #2
0
Файл: test.py Проект: chaby/dana
def newPipeline():
    checkArgumentMarkerReducer()
    m = DnaUtils.readIUPACFile(sys.argv[1])
    mapOligos = DnaUtils.readOligosFile(sys.argv[2], m)
    # for k in mapOligos:
    #     for e in mapOligos[k]:
    #         print(e)
    # sys.exit(1)
    readSingleFastQFile(sys.argv[4], 10, "log.txt", mapOligos, sys.argv[3])
Пример #3
0
def generatePlot():
    checkArgumentMarkerReducer()
    logger.debug("IUPAC File : " + sys.argv[2])
    iupacMap = DnaUtils.readIUPACFile(sys.argv[2])
    logger.debug("forward MarkerMap File : " + sys.argv[3])
    logger.debug("reverse MarkerMap File : " + sys.argv[4])
    forwardMarkerMap = DnaUtils.readOligosFile(sys.argv[3], iupacMap)
    reverseMarkerMap = DnaUtils.readOligosFile(sys.argv[4], iupacMap, True)

    rAllOutputFileName = sys.argv[6] + ".r.csv"
    fAllOutputFileName = sys.argv[6] + ".f.csv"

    fAll = {}
    rAll = {}

    for root, dirs, files in os.walk(sys.argv[5]):
        for f1le in files:
            filePath = os.path.join(sys.argv[5], f1le)
            logger.debug("file : " + filePath)
            f, r = DnaUtils.readmarker(filePath, forwardMarkerMap,
                                       reverseMarkerMap, sys.argv[6], False)

            mergeMap(rAll, r)
            mergeMap(fAll, f)

            indexOsPath = filePath.rfind(os.sep)
            if indexOsPath == -1:
                indexOsPath = 0
            else:
                indexOsPath += 1
            indexOfDot = filePath.rfind(".")
            if indexOfDot == -1:
                indexOfDot = len(filePath)
            rOutputFileName = filePath[indexOsPath:indexOfDot] + ".r.csv"
            fOutputFileName = filePath[indexOsPath:indexOfDot] + ".f.csv"
            DnaUtils.mapToCsv(r, rOutputFileName)
            DnaUtils.mapToCsv(f, fOutputFileName)

    DnaUtils.mapToCsv(rAll, rAllOutputFileName)
    DnaUtils.mapToCsv(fAll, fAllOutputFileName)
Пример #4
0
Файл: test.py Проект: chaby/dana
def generatePlot():
    checkArgumentMarkerReducer()
    logger.debug("IUPAC File : " +  sys.argv[2])
    iupacMap = DnaUtils.readIUPACFile(sys.argv[2])
    logger.debug("forward MarkerMap File : " +  sys.argv[3])
    logger.debug("reverse MarkerMap File : " +  sys.argv[4])
    forwardMarkerMap = DnaUtils.readOligosFile(sys.argv[3], iupacMap)
    reverseMarkerMap = DnaUtils.readOligosFile(sys.argv[4], iupacMap, True)
   
    rAllOutputFileName = sys.argv[6] + ".r.csv"
    fAllOutputFileName = sys.argv[6] + ".f.csv"
    
    fAll = {}
    rAll = {}
    
    for root, dirs, files in os.walk(sys.argv[5]):
        for f1le in files:
            filePath = os.path.join(sys.argv[5], f1le)
            logger.debug("file : " + filePath)
            f,r = DnaUtils.readmarker(filePath, forwardMarkerMap, reverseMarkerMap, sys.argv[6], False)
            
            mergeMap(rAll, r)
            mergeMap(fAll, f)
            
            indexOsPath = filePath.rfind(os.sep)
            if indexOsPath == -1:
                indexOsPath = 0
            else:
                indexOsPath += 1
            indexOfDot = filePath.rfind(".")
            if indexOfDot == -1:
                indexOfDot = len(filePath)
            rOutputFileName = filePath[indexOsPath:indexOfDot] + ".r.csv"
            fOutputFileName = filePath[indexOsPath:indexOfDot] + ".f.csv"
            DnaUtils.mapToCsv(r, rOutputFileName)
            DnaUtils.mapToCsv(f, fOutputFileName)
        
    DnaUtils.mapToCsv(rAll, rAllOutputFileName)
    DnaUtils.mapToCsv(fAll, fAllOutputFileName)